Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Kidney
Cell type
293
Primary Tissue
Kidney
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HEK293T
cell line
HEK293T
cell type
Human embryonic kidney
chip antibody
CTCF (Abcam, #ab128873)
geo_loc_name
missing
collection_date
missing

Sequenced DNA Library

library_name
GSM6611387
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a focused-ultrasonicator (Covaris). ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB #E7645). 200 ng of DNA was used as starting material for input and 4-60 ng for ip samples. length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
18699034
Reads aligned (%)
93.0
Duplicates removed (%)
12.9
Number of peaks
34929 (qval < 1E-05)

hg19

Number of total reads
18699034
Reads aligned (%)
92.6
Duplicates removed (%)
12.9
Number of peaks
34661 (qval < 1E-05)

Base call quality data from DBCLS SRA